Previous studies have reported higher dental fluorosis prevalence in high-altitude communities than in low-altitude communities. This investigation determined and compared dental fluorosis prevalence in populations of children living at high and low altitudes in Mexico. Fluorosis prevalence was determined in 7 to 10-year-old children: 67 in Mexico City (2,240 m) and 71 in Veracruz (sea level). Previous fluoride exposure of those children was surveyed by retrospective, questionnaire data. The fluoride content of water and salt from those communities was also documented. Fluorosis prevalence in Mexico City (53.0%) was significantly higher than in Veracruz (24.3%) (p < 0.0001). While there were statistical differences in one of the fluorosis risk factors between the two communities, the observed difference in fluorosis prevalence was still significant when data were analyzed after adjusting for the reported differences in that factor. Our results led to the conclusion that the difference in fluorosis prevalence in Mexico City and Veracruz could not be explained by differences in fluoride content of the salt or water samples, self-reported exposure to fluorosis risk factors or estimated fluoride intake.